In order to enable hierarchical wildcard search for lineage systems (e.g. to select all lineages descendant from mpox clade IIb lineage B.1), SILO needs to know the full lineage tree structure.
This repository contains those definitions for viruses supported by Pathoplexus that have hierarchical lineage systems.
The expected file format is documented here: https://github.com/GenSpectrum/LAPIS-SILO/blob/main/documentation/lineage_definitions.md
When making changes to lineage definitions, please ensure that:
lineages.yaml and put it in a folder with the timestamp of the corresponding Nextclade release. That’s because lineage definitions may change over time. The timestamp ensures we can easily track which Nextclade release a lineage definition corresponds to..lineageSystemDefinitions: https://github.com/pathoplexus/pathoplexus/blob/main/loculus_values/values.yaml.lineageSystemDefinitions: https://github.com/loculus-project/loculus/blob/main/kubernetes/loculus/values.yamlcchf/S/2025-09-12--03-01-02Z/lineages.yamlIt’s possible that new Nextclade releases don’t change the lineage definitions - in that case we don’t need to add a new folder.
Repo layout:
definitions/
<organism_short_name>/
<nextclade_release_timestamp>/
lineages.yaml
<multi_segmented_organism_short_name>/
<segment_or_pathogen_short_name>/
<nextclade_release_timestamp>/
lineages.yaml
Non-timestamped lineage definitions in this repository are deprecated and will be removed at some point in the future. Please use the timestamped definitions instead.